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' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $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' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $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' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $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' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $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' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $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' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $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' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $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' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $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' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $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' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $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' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $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' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $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' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $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' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $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' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $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' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $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' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $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' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $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' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $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' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $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' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $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' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $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' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $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' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $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' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $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' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $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' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $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' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $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' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $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' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $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' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $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' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $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' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $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' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $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' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $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' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $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' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $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' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $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' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $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' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $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' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $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' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $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' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $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' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $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' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $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' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $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' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $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' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $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' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $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' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $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' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $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' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $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' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $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' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $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' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $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' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $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' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $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' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $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' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $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' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $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' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $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' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $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' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $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' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $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' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $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' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $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' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $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' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $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' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $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' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $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' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $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' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $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' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $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' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $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' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $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' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $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' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $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' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $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' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $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' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $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' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $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' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $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' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $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' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $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' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $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' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $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' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $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' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $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' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $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' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $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' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $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' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $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' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $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' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $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' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $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' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $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' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $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' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $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' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $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' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $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' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $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' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $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' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $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' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $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' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $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' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $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' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $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' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $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' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $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' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $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' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $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' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $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' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $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' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $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' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $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' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $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' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $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' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $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' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $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' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $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' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $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' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $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' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $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' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $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' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $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' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $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' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $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' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $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' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $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' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $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' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $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' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $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' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $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' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $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' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $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' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $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' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $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' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $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' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $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' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $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' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $species_info = array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ) $local_species = 'pco' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $species_info = array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ) $local_species = 'pco' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $species_info = array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ) $local_species = 'ppe' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $species_info = array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ) $local_species = 'ppe' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $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' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $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' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $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' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $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' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $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' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $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' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $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' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $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' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $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' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $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' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $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' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $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' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $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' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $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' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $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' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $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' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $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' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $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' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $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' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $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' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $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' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $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' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $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' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $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' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $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' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $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' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $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' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $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' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $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' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $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' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $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' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $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' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $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' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $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' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $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' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $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' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $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' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $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' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $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' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $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' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $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' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $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' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $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' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $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' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $species_info = array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ) $local_species = 'vma' $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' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $species_info = array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ) $local_species = 'vma' $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' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $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' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $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' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $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' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $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' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $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' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $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' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $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' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ), 'gf_id' => 'HOM05D001136', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001136' ), 'data_identifier' => 'HOM05D001136', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001136', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p27380' => 'bna', 'A03p31250' => 'bna', 'A09p01540' => 'bna', 'Aa31LG11G7960' => 'aar', 'Aa31LG1G6070' => 'aar', 'Aa31LG1G9920' => 'aar', 'Aa31LG2G11530' => 'aar', 'Aa31LG5G1720' => 'aar', 'Aa31sc557G10' => 'aar', 'Aa31sc933G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1972' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1973' => 'aag', 'Actinidia02268' => 'ach', 'Actinidia13367' => 'ach', 'Actinidia16854' => 'ach', 'Actinidia21004' => 'ach', 'Actinidia21515' => 'ach', 'Actinidia35527' => 'ach', 'Ah.02g112220' => 'amhyb', 'Ah.04g154700' => 'amhyb', 'Ah.11g049300' => 'amhyb', 'AL1G11940' => 'aly', 'AL1G19650' => 'aly', 'AL1G65940' => 'aly', 'AL5G45310' => 'aly', 'AL6G51150' => 'aly', 'Aqoxy2G01832' => 'aox', 'Aqoxy2G02781' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00QZ3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASK093' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C3LD3D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CICU5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FC6Q2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JE21VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WKI8DK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WPQ881' => 'arhy', 'AT1G02620' => 'ath', 'AT1G09180' => 'ath', 'AT1G56330' => 'ath', 'AT3G62560' => 'ath', 'AT4G02080' => 'ath', 'ATR0693G164' => 'atr', 'ATR0693G247' => 'atr', 'Atru.chr2.153' => 'acertr', 'Atru.chr4.2946' => 'acertr', 'Atru.chr4.2978' => 'acertr', 'Atru.chr4.2984' => 'acertr', 'Atru.chr5.1020' => 'acertr', 'Atru.chr5.1029' => 'acertr', 'Atru.chr6.544' => 'acertr', 'AUR62000676' => 'cqu', 'AUR62005277' => 'cqu', 'AUR62011821' => 'cqu', 'AUR62016134' => 'cqu', 'AUR62024665' => 'cqu', 'AUR62033564' => 'cqu', 'AUR62041408' => 'cqu', 'AUR62041409' => 'cqu', 'BcaB01g02079' => 'bca', 'BcaB01g02417' => 'bca', 'BcaB04g20159' => 'bca', 'BcaB07g31120' => 'bca', 'BcaC01g06777' => 'bca', 'BcaC03g14170' => 'bca', 'BcaC04g22054' => 'bca', 'BcaC04g24034' => 'bca', 'BcaC04g24036' => 'bca', 'BcaC05g24774' => 'bca', 'BcaC06g31768' => 'bca', 'BcaC07g38484' => 'bca', 'BcaC09g49564' => 'bca', 'BolC1t03479H' => 'bol', 'BolC3t16096H' => 'bol', 'BolC5t29474H' => 'bol', 'BolC8t48892H' => 'bol', 'BolC9t53098H' => 'bol', 'BolC9t55325H' => 'bol', 'BraA01t02878Z' => 'bra', 'BraA03t12305Z' => 'bra', 'BraA06t23805Z' => 'bra', 'BraA09t35814Z' => 'bra', 'BraA09t37528Z' => 'bra', 'C01p35200' => 'bna', 'C03p38090' => 'bna', 'C09p01650' => 'bna', 'CAN.G1280.25' => 'can', 'CAN.G1715.14' => 'can', 'CAN.G197.9' => 'can', 'CAN.G777.6' => 'can', 'CANSAT25G3547' => 'cansat', 'CANSAT54G1820' => 'cansat', 'CANSAT78G0045' => 'cansat', 'CANSAT78G2009' => 'cansat', 'CARHR001910' => 'chi', 'CARHR009120' => 'chi', 'CARHR289870' => 'chi', 'Carub.0001s0166' => 'cru', 'Carub.0001s0850' => 'cru', 'Carub.0002s0783' => 'cru', 'Carub.0005s2921' => 'cru', 'Carub.0006s3514' => 'cru', 'Ca_01874_v3' => 'car', 'Ca_09299_v3' => 'car', 'Ca_10164_v3' => 'car', 'Ca_21454_v3' => 'car', 'CBR_g55006' => 'cbr', 'Cc01_g21340' => 'ccan', 'Cc02_g34850' => 'ccan', 'CDE02G1184' => 'cde', 'CDE05G3216' => 'cde', 'CDE08G1611' => 'cde', 'CDE11G0373' => 'cde', 'Cfa005812' => 'cfa', 'Cfa006689' => 'cfa', 'Cfa015343' => 'cfa', 'Cfa015344' => 'cfa', 'Ciclev10002566m.g' => 'ccl', 'Ciclev10005438m.g' => 'ccl', 'Ciclev10022379m.g' => 'ccl', 'CiPaw.01G140800' => 'cil', 'CiPaw.01G140900' => 'cil', 'CiPaw.02G076100' => 'cil', 'CiPaw.07G028400' => 'cil', 'CiPaw.07G116500' => 'cil', 'CiPaw.08G090600' => 'cil', 'CiPaw.08G156400' => 'cil', 'ClCG00G004390' => 'cla', 'ClCG02G015030' => 'cla', 'ClCG02G015050' => 'cla', 'ClCG06G004690' => 'cla', 'ClCG09G005150' => 'cla', 'ClCG10G011340' => 'cla', 'COL.COLO4_04145' => 'col', 'COL.COLO4_23244' => 'col', 'COL.COLO4_34654' => 'col', 'Cpa.g.sc18.28' => 'cpa', 'Cpa.g.sc48.146' => 'cpa', 'Cpa.g.sc929.2' => 'cpa', 'Cre11.g468300' => 'cre', 'CsaV3_2G006970' => 'csa', 'CsaV3_4G001160' => 'csa', 'CsaV3_6G022460' => 'csa', 'CsaV3_7G029920' => 'csa', 'CSS0003822' => 'camsi', 'CSS0003953' => 'camsi', 'CSS0005855' => 'camsi', 'CSS0007909' => 'camsi', 'CSS0012561' => 'camsi', 'CSS0024110' => 'camsi', 'CSS0025379' => 'camsi', 'CSS0034520' => 'camsi', 'CSS0036132' => 'camsi', 'CSS0043021' => 'camsi', 'CSS0047815' => 'camsi', 'DCAR_002901' => 'dca', 'DCAR_005766' => 'dca', 'DCAR_018313' => 'dca', 'DCAR_029359' => 'dca', 'Dinv10086' => 'din', 'Dinv24426' => 'din', 'Dinv30874' => 'din', 'Dinv33110' => 'din', 'Dinv44308' => 'din', 'Duzib052G0804' => 'dzi', 'Duzib106G1558' => 'dzi', 'Duzib128G1078' => 'dzi', 'Duzib133G0892' => 'dzi', 'Duzib151G0790' => 'dzi', 'Duzib151G1068' => 'dzi', 'Duzib177G0187' => 'dzi', 'Duzib211G0235' => 'dzi', 'ECA236G3601' => 'eca', 'EL10Ac3g05458' => 'bvu', 'EL10Ac4g09816' => 'bvu', 'EL10As5g23518' => 'bvu', 'Eucgr.A00205' => 'egr', 'Eucgr.A00206' => 'egr', 'Eucgr.A00207' => 'egr', 'Eucgr.A00208' => 'egr', 'Eucgr.A00209' => 'egr', 'Eucgr.A00210' => 'egr', 'Eucgr.A00323' => 'egr', 'Eucgr.A00324' => 'egr', 'Eucgr.A00325' => 'egr', 'Eucgr.A00327' => 'egr', 'Eucgr.A00328' => 'egr', 'Eucgr.A00331' => 'egr', 'Eucgr.A00332' => 'egr', 'Eucgr.A00334' => 'egr', 'Eucgr.A00335' => 'egr', 'Eucgr.A00336' => 'egr', 'Eucgr.A00337' => 'egr', 'Eucgr.A00338' => 'egr', 'Eucgr.A00339' => 'egr', 'Eucgr.A00341' => 'egr', 'Eucgr.A00342' => 'egr', 'Eucgr.A00343' => 'egr', 'Eucgr.A00344' => 'egr', 'Eucgr.A00345' => 'egr', 'Eucgr.A00346' => 'egr', 'Eucgr.A00347' => 'egr', 'Eucgr.H01051' => 'egr', 'Eucgr.H04036' => 'egr', 'Eucgr.K03541' => 'egr', 'Eucgr.L02065' => 'egr', 'Eucgr.L02066' => 'egr', 'Eucgr.L02068' => 'egr', 'Eucgr.L02069' => 'egr', 'FAN02G0774' => 'fan', 'FAN04G2480' => 'fan', 'FAN07G1402' => 'fan', 'FAN08G0230' => 'fan', 'FAN09G4513' => 'fan', 'FAN12G1532' => 'fan', 'FAN12G3788' => 'fan', 'FAN13G0974' => 'fan', 'FAN14G4795' => 'fan', 'FAN18G1732' => 'fan', 'FvH4_4g19410' => 'fve', 'FvH4_4g19420' => 'fve', 'FvH4_4g19421' => 'fve', 'FvH4_5g39351' => 'fve', 'FvH4_6g07290' => 'fve', 'Glyma.03G231800' => 'gma', 'Glyma.07G241800' => 'gma', 'Glyma.07G241900' => 'gma', 'Glyma.09G038200' => 'gma', 'Glyma.10G147800' => 'gma', 'Glyma.15G143300' => 'gma', 'Glyma.17G032000' => 'gma', 'Glyma.17G032100' => 'gma', 'Glyma.19G228800' => 'gma', 'Glyma.20G239600' => 'gma', 'Gohir.A02G053600' => 'ghi', 'Gohir.A08G040800' => 'ghi', 'Gohir.A08G119200' => 'ghi', 'Gohir.A08G206400' => 'ghi', 'Gohir.A10G170800' => 'ghi', 'Gohir.A11G271800' => 'ghi', 'Gohir.A12G125700' => 'ghi', 'Gohir.D02G058300' => 'ghi', 'Gohir.D02G065866' => 'ghi', 'Gohir.D08G050900' => 'ghi', 'Gohir.D08G140000' => 'ghi', 'Gohir.D08G223200' => 'ghi', 'Gohir.D10G158632' => 'ghi', 'Gohir.D10G177900' => 'ghi', 'Gohir.D11G085800' => 'ghi', 'Gohir.D11G282000' => 'ghi', 'Gohir.D12G129200' => 'ghi', 'Gohir.D13G114900' => 'ghi', 'Gorai.004G050500' => 'gra', 'Gorai.004G144100' => 'gra', 'Gorai.004G237100' => 'gra', 'Gorai.005G065800' => 'gra', 'Gorai.007G304600' => 'gra', 'Gorai.008G121900' => 'gra', 'Gorai.008G140300' => 'gra', 'Gorai.011G198700' => 'gra', 'Gorai.012G031000' => 'gra', 'Gorai.013G129100' => 'gra', 'GSVIVG01001640001' => 'vvi', 'GSVIVG01025197001' => 'vvi', 'GSVIVG01028107001' => 'vvi', 'GSVIVG01031224001' => 'vvi', 'GSVIVG01035025001' => 'vvi', 'HanXRQChr03g0071101' => 'han', 'HanXRQChr10g0285301' => 'han', 'HanXRQChr11g0340891' => 'han', 'HanXRQChr15g0464161' => 'han', 'Haze_01268' => 'cav', 'Haze_01269' => 'cav', 'Haze_04076' => 'cav', 'Haze_05030' => 'cav', 'Haze_27592' => 'cav', 'Hma1.2p1_0008F-1.1_g005740' => 'hma', 'Hma1.2p1_0078F.1_g040080' => 'hma', 'Hma1.2p1_0472F.1_g159910' => 'hma', 'Hma1.2p1_0486F.1_g163130' => 'hma', 'HPP92_010934' => 'vpl', 'HPP92_018270' => 'vpl', 'Hund03108' => 'sun', 'Hund07138' => 'sun', 'Hund09624' => 'sun', 'Hund11956' => 'sun', 'Hund11957' => 'sun', 'Lalb_Chr04g0260451' => 'lal', 'Lalb_Chr06g0167491' => 'lal', 'Lalb_Chr07g0182131' => 'lal', 'Lalb_Chr07g0182141' => 'lal', 'Lalb_Chr12g0200941' => 'lal', 'Lalb_Chr13g0298371' => 'lal', 'Lalb_Chr15g0077661' => 'lal', 'Lalb_Chr15g0089281' => 'lal', 'Lalb_Chr15g0089291' => 'lal', 'Lalb_Chr18g0046071' => 'lal', 'Lalb_Chr20g0120931' => 'lal', 'Lalb_Chr20g0120941' => 'lal', 'Lj1g0009477' => 'lja', 'Lj4g0016267' => 'lja', 'Lj5A336T41' => 'lonja', 'Lj5g0012226' => 'lja', 'Lj6C688T13' => 'lonja', 'Lj6g0021970' => 'lja', 'Lj9C218T9' => 'lonja', 'Lju926A12G23' => 'lonja', 'Lsat_1_v5_gn_7_74660' => 'lsa', 'Lsat_1_v5_gn_8_166460' => 'lsa', 'Lsat_1_v5_gn_9_122660' => 'lsa', 'Manes.01G227000' => 'mes', 'Manes.03G202300' => 'mes', 'Manes.05G002700' => 'mes', 'Manes.08G112100' => 'mes', 'Manes.08G112200' => 'mes', 'Manes.09G176100' => 'mes', 'Manes.15G005900' => 'mes', 'Mapoly0082s0086' => 'mpo', 'MBI10_g34305_MAGBIO' => 'mbi', 'MBI17_g34575_MAGBIO' => 'mbi', 'MBI19_g24820_MAGBIO' => 'mbi', 'MCO12G265' => 'mco', 'MD02G1080500' => 'mdo', 'MD03G1296300' => 'mdo', 'MD04G1194800' => 'mdo', 'MD11G1315700' => 'mdo', 'MD12G1207000' => 'mdo', 'MD16G1157700' => 'mdo', 'MD16G1157800' => 'mdo', 'Medtr2g034640' => 'mtr', 'Medtr4g121860' => 'mtr', 'Medtr5g098820' => 'mtr', 'Medtr7g112090' => 'mtr', 'MELO3C004196.2' => 'cme', 'MELO3C015929.2' => 'cme', 'MELO3C017922.2' => 'cme', 'MELO3C021279.2' => 'cme', 'Migut.D00089' => 'egut', 'Migut.G00092' => 'egut', 'Migut.N01388' => 'egut', 'MSTRG.10140' => 'ama', 'MSTRG.18109' => 'ama', 'MSTRG.20381' => 'ama', 'MSTRG.21680' => 'ama', 'MSTRG.21778' => 'ama', 'MSTRG.27947' => 'ama', 'Nitab4.5_0000155g0020' => 'nta', 'Nitab4.5_0000363g0290' => 'nta', 'Nitab4.5_0000368g0230' => 'nta', 'Nitab4.5_0001301g0040' => 'nta', 'Nitab4.5_0001305g0030' => 'nta', 'Nitab4.5_0003294g0020' => 'nta', 'Nitab4.5_0006144g0020' => 'nta', 'Nitab4.5_0007747g0040' => 'nta', 'Nitab4.5_0013342g0010' => 'nta', 'Nn3g18030' => 'nnu', 'Nn3g21667' => 'nnu', 'Nn4g23834' => 'nnu', 'Nn4g25622' => 'nnu', 'Nn5g27721' => 'nnu', 'Oeu000017.1' => 'oeu', 'Oeu005865.1' => 'oeu', 'Oeu008465.1' => 'oeu', 'Oeu036982.1' => 'oeu', 'Oeu038016.1' => 'oeu', 'Oeu062258.1' => 'oeu', 'Oeu064167.1' => 'oeu', 'Oeu064810.3' => 'oeu', 'Os01g0254000' => 'osa', 'Os01g0338000' => 'osa', 'Os06g0225000' => 'osa', 'Os12g0560300' => 'osa', 'Peaxi162Scf00058g02912' => 'pax', 'Peaxi162Scf00065g00116' => 'pax', 'Peaxi162Scf00673g00136' => 'pax', 'Peaxi162Scf00691g00005' => 'pax', 'PGR031G0033' => 'pgr', 'PGR031G1063' => 'pgr', 'PGR044G1383' => 'pgr', 'PGSC0003DMG400002778' => 'stu', 'PGSC0003DMG400007288' => 'stu', 'PGSC0003DMG400009038' => 'stu', 'PGSC0003DMG400026695' => 'stu', 'Phvul.001G225400' => 'pvu', 'Phvul.003G112000' => 'pvu', 'Phvul.003G112100' => 'pvu', 'Phvul.009G254700' => 'pvu', 'Potri.005G015400' => 'ptr', 'Potri.005G019100' => 'ptr', 'Potri.008G107800' => 'ptr', 'Potri.010G141900' => 'ptr', 'Potri.013G009900' => 'ptr', 'Potri.013G010000' => 'ptr', 'Pp3c20_15600' => 'ppa', 'Pp3c23_6490' => 'ppa', 'Pp3c2_12620' => 'ppa', 'Pp3c2_5480' => 'ppa', 'PRCOL_00002548' => 'pco', 'Prupe.1G122600' => 'ppe', 'Prupe.1G122700' => 'ppe', 'Prupe.6G314700' => 'ppe', 'Prupe.8G271000' => 'ppe', 'Psat1g160680' => 'psa', 'Psat3g012960' => 'psa', 'Psat4g022240' => 'psa', 'PSO063G2508' => 'pso', 'PSO170G4372' => 'pso', 'PSO210G0635' => 'pso', 'PSO210G7346' => 'pso', 'PSO357G0525' => 'pso', 'PSO541G6122' => 'pso', 'PSO675G7115' => 'pso', 'PSO761G0169' => 'pso', 'PSO761G0244' => 'pso', 'PSO832G1167' => 'pso', 'QL03p018321' => 'qlo', 'QL03p018364' => 'qlo', 'QL03p018374' => 'qlo', 'QL03p018381' => 'qlo', 'QL03p018432' => 'qlo', 'QL03p018445' => 'qlo', 'QL03p018468' => 'qlo', 'QL03p018473' => 'qlo', 'QL03p018510' => 'qlo', 'QL03p018523' => 'qlo', 'QL06p011548' => 'qlo', 'QL06p011553' => 'qlo', 'QL08p063591' => 'qlo', 'QL12p020140' => 'qlo', 'RcHm_v2.0_Chr2g0113571' => 'rch', 'RcHm_v2.0_Chr2g0145331' => 'rch', 'RcHm_v2.0_Chr3g0456901' => 'rch', 'RcHm_v2.0_Chr3g0488041' => 'rch', 'RcHm_v2.0_Chr4g0424441' => 'rch', 'RcHm_v2.0_Chr4g0424451' => 'rch', 'RcHm_v2.0_Chr4g0424461' => 'rch', 'RcHm_v2.0_Chr4g0424521' => 'rch', 'RcHm_v2.0_Chr4g0424561' => 'rch', 'RcHm_v2.0_Chr7g0225711' => 'rch', 'RcHm_v2.0_Chr7g0225741' => 'rch', 'RcHm_v2.0_Chr7g0225771' => 'rch', 'RcHm_v2.0_Chr7g0225801' => 'rch', 'RcHm_v2.0_Chr7g0225921' => 'rch', 'RcHm_v2.0_Chr7g0241641' => 'rch', 'Rhsim02G0005400' => 'rsi', 'Rhsim04G0233700' => 'rsi', 'Rhsim05G0133200' => 'rsi', 'Rhsim11G0094400' => 'rsi', 'Sabra05G0012700' => 'sbr', 'Sabra05G0025400' => 'sbr', 'Sabra05G0025500' => 'sbr', 'Sabra08G0081500' => 'sbr', 'Sabra10G0109700' => 'sbr', 'Sabra13G0008400' => 'sbr', 'Sabra13G0008500' => 'sbr', 'SalBow2G0574' => 'sbo', 'SalBow3G1149' => 'sbo', 'SalBow3G2511' => 'sbo', 'SalBow7G0372' => 'sbo', 'SalBow8G2108' => 'sbo', 'SalBow8G4410' => 'sbo', 'Sc05g0000480' => 'sci', 'Sc06g0005780' => 'sci', 'Sc13g0006400' => 'sci', 'Sc16g0008960' => 'sci', 'Sc17g0000510' => 'sci', 'Sed0001673' => 'sed', 'Sed0010648' => 'sed', 'Sed0011077' => 'sed', 'Sed0016190' => 'sed', 'Sed0020647' => 'sed', 'SEGI_03403' => 'sgi', 'SEGI_10169' => 'sgi', 'SEGI_24364' => 'sgi', 'SGA_v2.0_scaffold119G32668' => 'sas', 'SGA_v2.0_scaffold198G41123' => 'sas', 'SGA_v2.0_scaffold264G46040' => 'sas', 'SGA_v2.0_scaffold334G49061' => 'sas', 'SGA_v2.0_scaffold36G14325' => 'sas', 'SGA_v2.0_scaffold376G50274' => 'sas', 'SGA_v2.0_scaffold80G25878' => 'sas', 'SGA_v2.0_scaffold81G26128' => 'sas', 'SHI20087' => 'shi', 'SMO239G0100' => 'smo', 'SMO358G0663' => 'smo', 'Solyc01g060130.3' => 'sly', 'Solyc01g100350.3' => 'sly', 'Solyc06g009660.3' => 'sly', 'Sopen01g026280' => 'spe', 'Sopen01g031310' => 'spe', 'Sopen01g043870' => 'spe', 'Sopen06g004300' => 'spe', 'Sp1g01620' => 'spa', 'Sp1g07800' => 'spa', 'Sp2g06540' => 'spa', 'Sp2g06570' => 'spa', 'Sp5g00940' => 'spa', 'Sp6g01970' => 'spa', 'TAR362G0690' => 'tar', 'TAR365G0223' => 'tar', 'TAR371G0861' => 'tar', 'TAR633G0579' => 'tar', 'TAR633G2824' => 'tar', 'TAR636G1408' => 'tar', 'TAR636G2107' => 'tar', 'THA.LOC104801303' => 'tha', 'THA.LOC104802197' => 'tha', 'THA.LOC104802702' => 'tha', 'THA.LOC104808008' => 'tha', 'THA.LOC104816883' => 'tha', 'THA.LOC104820680' => 'tha', 'THA.LOC104827090' => 'tha', 'Thecc.01G312000' => 'tca', 'Thecc.04G296800' => 'tca', 'Thecc.04G296900' => 'tca', 'Thecc.05G321500' => 'tca', 'Thhalv10002861m.g' => 'esa', 'Thhalv10006249m.g' => 'esa', 'Thhalv10008842m.g' => 'esa', 'Thhalv10008843m.g' => 'esa', 'Thhalv10023657m.g' => 'esa', 'Thhalv10023704m.g' => 'esa', 'Thhalv10028985m.g' => 'esa', 'TPR.G1607' => 'tpr', 'TPR.G3977' => 'tpr', 'TPR.G5782' => 'tpr', 'TWI09G0415' => 'twi', 'TWI18G0938' => 'twi', 'TWI36G1652' => 'twi', 'TWI53G1932' => 'twi', 'TWI73G0414' => 'twi', 'TWI73G0784' => 'twi', 'TWI75G1112' => 'twi', 'vmacro01556' => 'vma', 'vmacro15191' => 'vma', 'vmacro19725' => 'vma', 'VMungo0645G0001' => 'vmu', 'VMungo1215G1843' => 'vmu', 'VMungo1309G0133' => 'vmu', 'VMungo1383G2354' => 'vmu', 'Zm00001eb127670' => 'zma', 'Zm00001eb131280' => 'zma', 'Zm00001eb168590' => 'zma', 'Zm00001eb340890' => 'zma' ) $gf_id = 'HOM05D001136' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001136' ) $data_identifier = 'HOM05D001136' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 7, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 6, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 33, 'fan' => (int) 10, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 10, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 5, 'lal' => (int) 12, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 10, 'qlo' => (int) 14, 'rch' => (int) 15, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 7, 'tpr' => (int) 3, 'twi' => (int) 7, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb340890' $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